In the acknowledgements to this masterful piece of modern history a name stands out. That of Don DeLillo. In his thanks Shenon marvels at how close DeLillo's fiction came to the truth about the Kennedy murder and the Warren Commission which was set up to get to the truth of what happened on that day in Dallas.

The book even takes its subtitle– The Secret History of the Kennedy Assassination – from the name of a report written within Libra by the character Nicholas Branch. It is Branch, a retired CIA analyst, who describes the Warren Report as "the megaton novel James Joyce would have written if he'd moved to Iowa City and lived to a hundred", a document "[so] lost to syntax and other arrangements, that it resembles a kind of mind-spatter".

This 600-plus page investigation by Shenon is an attempt to rationalise and understand the mind-spatter of the report and discover what went into it. And more importantly, what didn't. It's less a secret history of the shooting than of the commission itself. Shenon's previous work, The commission, did much the same about 9/11 own federal investigation.

Days after the killing, as conspiracy theories were already beginning to swarm regarding plots by the Cuban and Soviet governments, President Lyndon Johnson wanted to nip them in the bud. Using "the treatment", his legendary method of persuasion – a mixture of intimidation and persuasion conducted centimetres from a target's face – Johnson persuaded an extremely reluctant Supreme Court Chief Justice, Earl Warren, to run a vast federal commission into the murder to prove what every government agency publicly believed, that Lee Harvey Oswald was a deranged lone wolf.

The commission is a key part of Kennedy history now (DeLillo has called it the "Oxford English Dictionary of the assassination") – with its members variously scrutinised and accused of being part of a vast conspiracy. They included the former CIA director Allen Dulles, future president Gerald Ford (the FBI's inside man on the panel) and the segregationist Georgia senator, Richard Russell.

But they are mere supporting characters here. Having written so diligently about 9/11, the former New York Times man was approached anonymously by one of the junior lawyers on the commission to tell their – mostly unheard – story.

Due to the busy schedules of the commissioners themselves (Warren was running the Supreme Court in one of the key periods in its history), much of the commission's legwork was done by the young lawyers appointed to review each aspect of the assassination – from Oswald's background through to the role of the CIA and FBI. It was these young Ivy League hotshots, such as the future Senator Arlen Specter – father of the single-bullet theory – who uncovered most of the facts included (or not) – in the final 26-volume report. Many of these men are still alive and it is their testimony, alongside many others, which forms the backbone of this story – that of several well-meaning young men trying to find the truth in a morass of lies.

What Shenon reveals is not the vast conspiracy imagined by some, but just the sheer scale of confusion regarding the events in Dallas at the time and the many half-truths, back-covering and evasions which allowed the conspiracy to fester. He uncovers documents and stories which either made it nowhere near the Commission or – if they did – were blocked.

The biggest of these pertains to the federal agencies' tracking of Oswald while he visited Mexico City in 1963. It is not the conspiracy imagined in Oliver Stone's execrable film JFK, but it is a hall or mirrors which will never be fully understood due to the inexplicable contemporary decisions of some key figures (medical notes destroyed; Warren refusing to allow the autopsy pictures in the report) as well as the professional obfuscation of figures like the FBI's J Edgar Hoover and CIA "mole-hunter" James Angleton.

But this may be the closest we get to a map of that hall of mirrors. A Cruel and Shocking Act contains more revelations than can be written here. And, given the short, thriller-like chapters, they would feel like spoilers. Even his asides reek of deep reporting. We learn, for instance, that a CIA staffer in Mexico City served in the OSS (the CIA's precursor) with an agent Julia McWilliams, best known to millions as the celebrated chef Julia Child.

There is enough uncovered here to give the JFK "truthers" another 50 years of speculation, but that is thanks to the details and errors revealed by the author. It is a sober, gripping study of one of history's most overstudied moments, a work fit to rank alongside the previous masterpiece of the murder, William Manchester's Death of A President.